Hasan Otu

Avatar for Hasan Otu

Hasan Otu

Professor Electrical & Computer Engineering University of Nebraska-Lincoln

Contact

Address
Scott Engineering Center, Room C290D
Phone
402-472-3771 On-campus 2-3771
Email
hotu2@unl.edu
Website
Website
Website

Dr. Otu's research focuses on bioinformatics, computational and systems biology, and network science. He develops probabilistic graph and machine learning methods that integrate data-driven inference with external biological knowledge to reconstruct molecular interaction networks and analyze multi-omics data. His research addresses problems in biomarker discovery, feature selection, and mechanistic and predictive modeling, with applications spanning human health and disease, microbial communities, and plant systems.

Dr. Otu received his B.S. (1996) and M.S. (1997) degrees in Electrical and Electronics Engineering from Boğaziçi University and his Ph.D. in Electrical Engineering from the University of Nebraska–Lincoln in 2002. Before joining UNL in 2013, he held faculty appointments at Harvard Medical School (2003–2012), where he founded the Bioinformatics Core at Beth Israel Deaconess Medical Center and served as Associate Director of the Proteomics Core at Dana-Farber/Harvard Cancer Center. He was also the founding chair of the Department of Genetics and Bioengineering at Istanbul Bilgi University (2010–2013).

Dr. Otu has authored ~90 peer-reviewed journal articles, ~50 conference proceedings, a bioinformatics textbook, and several book chapters, and is an inventor on five U.S. patents.

Areas of Research and Professional Interest

  • Bioinformatics and Computational Biology
  • Systems Biology and Network Science
  • Bayesian Networks and Probabilistic Graphical Models
  • Machine Learning and Feature Selection
  • Multi-Omics Integration and Molecular Network Inference
  • Biomarker Discovery and Mechanistic Modeling

Education

  • Ph.D., Electrical Engineering, University of Nebraska-Lincoln, 2002
  • M.S., Electrical and Electronics Engineering, Bogazici University, 1997
  • B.S., Electrical and Electronics Engineering, Bogazici University, 1996

Experience

Academic Appointments

  • 2013-present, Professor - University of Nebraska-Lincoln, Department of Electrical and Computer Engineering
  • 2010-2013, Assistant Prof. - Istanbul Bilgi University Department of Bioengineering, Istanbul, Turkey
  • 2003- 2012, Instructor of Medicine - Harvard Medical School, Boston, MA
  • 2002-2003, Research Fellow - Harvard Medical School, Boston, MA
  • 2000-2002, Instructor of EE - University of Nebraska-Lincoln, Department of Electrical Engineering

Major Administrative Responsibilities

  • 2026–present, Chair, College of Engineering Promotion and Tenure Committee, UNL
  • 2025–present, Chair, ECE Promotion and Tenure Committee, UNL
  • 2023–2026, Faculty Senator, UNL
  • 2017–2022, ECE Executive Committee, UNL (Chair, 2020–2022)
  • 2010–2013, Founding Chair, Department of Bioengineering, Istanbul Bilgi University
  • 2004–2012, Associate Director, Proteomics Core, Dana-Farber/Harvard Cancer Center
  • 2003–2012, Founding Director and subsequently Associate Director, Bioinformatics Core, Beth Israel Deaconess Medical Center

Editorial Boards and Program Committees

  • 2023- : Editorial Board Member - Frontiers in Plant Science - Plant Bioinformatics
  • 2020- : Associate Editor - Cells
  • 2018- 2020: Associate Editor - Advances in Bioinformatics
  • 2017: Member - Program Committee International Symposium on Integrative Bioinformatics
  • 2017: Member - Technical Program Committee Electro-Information Technology Conference
  • 2014- : Associate Editor - Journal of Bioinformatics, Proteomics and Imaging Analysis
  • 2014-2019: Editor in Chief - Journal of Bioinformatics, Computational and Systems Biology
  • 2013-2017: Associate Editor - Advances in Biology
  • 2012: Organizer - Workshop, “Bioinformatics Approaches for Analysis of High-throughput Biological Data”, International Centre for Genetic Engineering and Biotechnology (ICGEB)
  • 2011: Program Committee Co-chair The 6th International Symposium on Health Informatics and Bioinformatics, (HIBIT)
  • 2010-2017: Associate Editor - EURASIP Journal on Bioinformatics and Systems Biology

Selected Publications

  • Omede MD*, Otu HH*, Grossberg LB, Huang JY, Gu X, Dillon ST, Can H, Morhardt TL, Pursley K, Winter HS, Libermann TA. “Serum proteomics in paediatric inflammatory bowel disease from a case-control study: biomarker discovery and ulcerative colitis-Crohn's disease differentiation” eBioMedicine, 2026; 128:106311. (*Equal contributors) Link
  • Tripp BA, Dillon ST, Yuan M, Asara JM, Vasunilashorn SM, Fong TG, Inouye SK, Ngo LH, Marcantonio E, Xie Z, Libermann T, Otu HH. “Integrated multi-omics analysis of cerebrospinal fluid in postoperative delirium” Biomolecules, 2024; 14(8):924. Link
  • Can H*, Chanumolu SK, Nielsen B, Alvarez S, Naldrett MJ, Unlu G, Otu HH*. “Integration of Meta-Multi-Omics Data Using Probabilistic Graphs and External Knowledge” Cells, 2023; 12(15):1998. (*Corresponding authors) Link
  • Chanumolu SK, Otu HH. “Identifying large scale interaction atlases using probabilistic graphs and external knowledge” J. Clin. Transl. Sci., 2022; 6(1):e27. Link
  • Tripp BA, Otu HH. “Integration of Multi-omics Data Using Probabilistic Graph Models and External Knowledge” Current Bioinformatics, 2022; 17(1):37-47. Link
  • Tripp BA, Dillon ST, Yuan M, Asara JM, Vasunilashorn SM, Fong TG, Inouye SK, Metzger ED, Xie Z, Ngo LH, Marcantonio E, Libermann T, Otu HH. “Targeted metabolomics analysis identifies risk and disease markers of postoperative Delirium” Scientific Reports, 2021; 11(1):1521. Link
  • Chanumolu SK, Albahrani M, Can H, Otu HH. “KEGG2Net: deducing gene interaction networks and acyclic graphs from KEGG pathways” EMBnet.journal, 2021, 26:e949. Link
  • Yalcin D, Otu HH. “An unbiased predictive model to detect DNA methylation propensity of CpG islands in the human genome” Current Bioinformatics, 2021; 16(2):179-196. Link
  • Chanumolu SK, Albahrani M, Otu HH. “FQStat: a parallel architecture for very high-speed assessment of sequencing quality metrics” BMC Bioinformatics, 2019 20(1):424. Link
  • Gonzalez-Muñoz E, Arboleda-Estudillo Y, Otu HH, Cibelli JB. “Histone chaperone ASF1A is required for maintenance of pluripotency and cellular reprogramming” Science, 2014; 345(6198):822-825. Link
  • Korucuoglu M, Isci S, Ozgur A, Otu HH. “Bayesian Pathway Analysis of Cancer Microarray Data” PLoS One, 2014; 9(7): e102803. Link
  • Dogan H, Can H, Otu HH. “Whole Genome Sequencing of a Turkish Individual” PLoS One, 2014; 9(1): e85233. Link
  • Isci S, Dogan H, Ozturk C, Otu HH. “Bayesian Network Prior: Network Analysis of Biological Data Using External Knowledge” Bioinformatics, 2014; 30(6):860-867. Link
  • Isci S, Jones J, Ozturk C, Otu HH. “Pathway analysis of high throughput biological data within a Bayesian Network framework” Bioinformatics, 2011; 27(12):1667-1674. Link
  • Al-Swailem AM , Shehata MM, Abu-Duhier FM, Al-Yamani EJ, Al-Busadah KA, Al-Arawi MS, Al-Khider AY, Al-Muhaimeed AN, Al-Qahtani FH, Al-Manee MM, Al-Shomrani BM, Al-Qhtani SM, Al-Harthi AS, Akdemir KC, Inan MS, Otu HH. “Sequencing, analysis, and annotation of expressed sequence tags for camelus dromedaries” PLoS ONE, 2010; 5(5):e10720. Link
  • Otu HH, Naxerova K, Can H, Ho K, Nesbitt N, Libermann TA, Karp SJ. “Restoration of liver mass after injury requires proliferative and not embryonic transcriptional patterns” Journal of Biological Chemistry, 2007; 282(15):11197-204. Link
  • Steidl U, Rosenbauer F, Verhaak RGW, Gu X, Ebralidze A., Otu HH, Klippel S, Steidl C, Bruns I, Costa DB, Wagner K, Aivado M, Kobbe G, Valk PJ, Passegué E, Libermann TA, Delwel R, Tenen DG. “Essential role of Jun family transcription factors in PU.1 knockdown-induced leukemic stem cells” Nature Genetics, 2006; 38(11):1269-77. Link
  • Kocabas AM, Crosby J, Ross PJ, Otu HH, Beyhan Z, Can H, Leong TW, Rosa GJM, Halgren RG, Lim B, Fernandez E and Cibelli JB. “The transcriptome of human oocytes” Proceedings of the National Academy of Sciences, 2006; 103: 14027-14032. Link
  • Otu HH, Sayood K. “A new sequence distance measure for phylogenetic tree construction” Bioinformatics 2003; 19(16):2122-2130. Link
  • Fortunel NO*, Otu HH*, Ng HH*, Chen J, Mu X, Chevassut T, Li X, Joseph M, Bailey C, Hatzfeld JA, Usta F, Vega VB, Long PM, Liberman TA, Lim B. “Comment on ‘Stemness: Transcriptional Profiling of Embryonic and Adult Stem Cells’ and ‘A Stem Cell Molecular Signature’” Science 2003; 302:393b. (*Equal contributors) Link

Complete publication list